WikiPathways Test: Metabolites and Metabolic Interactions (Homo sapiens)

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Revision as of 19:33, 4 December 2016 by AlexanderPico (Talk | contribs)
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1, 2VALID IDENTIFIERSMetabolites with identifiers in properly annotated datasources and valid values.Expected output:- full list of identifiers in the Backpage- links out all workingVersion 4 (2016-05-15)Acetic acid1. Double click this Metabolite DataNode and verifythat "Glucose" gives search results.Aspirin (HMDB)Old PubChem DB idDEPRECATED DATA SOURCESMetabolites with identifiers in with deprecated datasource strings.Optional output:- full list of identifiers in the Backpage- links out all workingSPECIAL METABOLITESThese metabolites are special in some way, for example,because they constitute a metabolite class.Expected output:- 1:n (directed) mappings to HMDB, ChemSpider, etcAspirin (KEGG)Aspirin (ChEBI, number only)Aspirin (CAS)Aspirin (PubChem)Aspirin (ChemSpider)long chain fatty acids (ChEBI)Enterobactin (not in HMDB)Aspirin (ChEBI, with prefix)Old KEGG DB idAspirin (Wikidata)Aspirin (InChIKey)Gibberellin A1 (KNApSAcK)ACE Inhibitor (ChEBI)Acetate


Description

This is a test pathway, to be used to test mappings to other databases, old system codes, etc. Each time a new metabolite mapping database is loaded onto the BridgeDb webservice that supports the linking on WikiPathways, this pathway should be opened and tested. The pathway has notes of the expected outcome.

Quality Tags

Ontology Terms

 

Bibliography

  1. van Iersel MP, Pico AR, Kelder T, Gao J, Ho I, Hanspers K, Conklin BR, Evelo CT; ''The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services.''; BMC Bioinformatics, 2010 PubMed Europe PMC Scholia
  2. Slenter DN, Kutmon M, Hanspers K, Riutta A, Windsor J, Nunes N, Mélius J, Cirillo E, Coort SL, Digles D, Ehrhart F, Giesbertz P, Kalafati M, Martens M, Miller R, Nishida K, Rieswijk L, Waagmeester A, Eijssen LMT, Evelo CT, Pico AR, Willighagen EL; ''WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research.''; Nucleic Acids Res, 2018 PubMed Europe PMC Scholia
  3. Gao J, Zhang C, van Iersel M, Zhang L, Xu D, Schultz N, R Pico A; ''BridgeDb app: unifying identifier mapping services for Cytoscape.''; F1000Res, 2014 PubMed Europe PMC Scholia
  4. Kell DB, Goodacre R; ''Metabolomics and systems pharmacology: why and how to model the human metabolic network for drug discovery.''; Drug Discov Today, 2014 PubMed Europe PMC Scholia
  5. Wishart DS; ''Emerging applications of metabolomics in drug discovery and precision medicine.''; Nat Rev Drug Discov, 2016 PubMed Europe PMC Scholia

History

View all...
CompareRevisionActionTimeUserComment
107656view09:06, 25 October 2019DeSlChanged HMDB and CHEBI IDs back to original (were changed due to bot).
107134view14:21, 17 September 2019MaintBotChEBI identifier normalization
106385view14:30, 28 August 2019DeSlSmall layout changes
106200view12:09, 16 August 2019MaintBotHMDB identifier normalization
104196view14:07, 9 May 2019DeSlUpdated character in lit refs.
104195view14:02, 9 May 2019DeSlUpdated DrugBank identifier.
103428view12:29, 28 February 2019DeSlUpdated layout
103426view12:26, 28 February 2019DeSlAdded new test for metabolic interaction mapping files.
103058view11:53, 7 February 2019DeSlEnterobacterin is part of HMDB now, changed note in DataNode on this.
103050view10:52, 7 February 2019DeSlAdded name for IUPHAR database manually (waiting for new release of bridgeDb).
103049view10:51, 7 February 2019DeSlAdded checks for ChEMBL, Drugbank and IUPHAR.
102473view09:21, 24 December 2018DeSlAdded latest WPs paper as reference
102472view09:17, 24 December 2018DeSlAdded 2 new tests, changed layout
98035view10:57, 5 July 2018DeSlAdded new testcase for recently added LIPID Maps IDs to wikidata
98034view09:54, 5 July 2018DeSlAdded correct ID for latest testcase.
98033view09:46, 5 July 2018DeSlAdded lit. ref to BridgeDb paper and BridgeDb Cytoscape app paper.
98032view09:43, 5 July 2018DeSlChanged version number.
98031view09:41, 5 July 2018DeSlAdded more testcases
95851view14:52, 26 January 2018DeSlAdded node to check mapping to old and new HMDB IDs.
92873view08:07, 12 July 2017EgonwAdded an EPA CompTox test case.
90665view19:33, 4 December 2016AlexanderPicoModified title
85438view09:46, 15 May 2016EgonwAdded two review papers about metabolomics.
85430view09:30, 15 May 2016EgonwAdded quotes around "Glucose".
85429view09:27, 15 May 2016EgonwSome tweaks, and "released" as version 4.
85428view09:27, 15 May 2016EgonwRemoved redundant new lines.
85427view09:21, 15 May 2016EgonwAdded MOM test cases.
85076view06:33, 12 April 2016EgonwAdded a KNApSAcK test.
84782view10:07, 20 March 2016EgonwReverted to version '20:28, 17 July 2015' by Egonw
84480view20:41, 25 February 2016AlexanderPicoReverted to version '13:36, 25 February 2016' by AlexanderPico
84479view20:41, 25 February 2016AlexanderPico
84478view20:36, 25 February 2016AlexanderPicoQuick edit to datanode annotation or property
81054view20:28, 17 July 2015EgonwHacked in the InChIKey DataSource via the GPML.
81053view20:27, 17 July 2015EgonwAn InChIKey node.
81052view20:14, 17 July 2015EgonwHacked in the Wikidata DataSource via the GPML.
81051view20:12, 17 July 2015EgonwAdded a Wikidata node (for future testing).
80972view13:53, 6 July 2015EgonwModified description
72071view18:10, 24 October 2013EgonwModified description
72070view18:09, 24 October 2013EgonwNew pathway

External references

DataNodes

View all...
NameTypeDatabase referenceComment
1. Double click this Metabolite DataNode and verify that "Glucose" gives search results.Metabolite
ACE Inhibitor (ChEBI)MetaboliteCHEBI:35457 (ChEBI)
AcetateMetaboliteCHEBI:30089 (ChEBI)
Acetic acidMetaboliteCHEBI:15366 (ChEBI)
Aspirin (CAS)Metabolite50-78-2 (CAS)
Aspirin (ChEBI, number only)Metabolite15365 (ChEBI)
Aspirin (ChEBI, with prefix)MetaboliteCHEBI:15365 (ChEBI)
Aspirin (ChemSpider)Metabolite2157 (Chemspider)
Aspirin (HMDB)MetaboliteHMDB01879 (HMDB)
Aspirin (InChIKey)MetaboliteBSYNRYMUTXBXSQ-UHFFFAOYSA-N (InChIKey)
Aspirin (KEGG)MetaboliteC01405 (KEGG Compound)
Aspirin (PubChem)Metabolite2244 (PubChem-compound)
Aspirin (Wikidata)MetaboliteQ18216 (Wikidata)
Enterobactin (not in HMDB)MetaboliteCHEBI:4799 (ChEBI)
Gibberellin A1 (KNApSAcK)MetaboliteC00000001 (KNApSAcK)
Old KEGG DB idMetabolite2244 (Kegg Compound)
Old PubChem DB idMetabolite2244 (PubChem)
long chain fatty acids (ChEBI)MetaboliteCHEBI:15904 (ChEBI)

Annotated Interactions

No annotated interactions

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